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Test SRA workflow with cromwell #25

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Merged
yxu-lanl merged 1 commit into from
Jan 24, 2025
Merged

Test SRA workflow with cromwell #25

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26 changes: 23 additions & 3 deletions installation/install.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -24,12 +24,32 @@ if [ ! -d $io_home ]; then
mkdir ${io_home}/${dir}
done

test_data_home=$app_home/workflows/Nextflow/test_data
if [ -d $test_data_home ]; then
ln -s ${test_data_home} ${io_home}/public/nextflow
cromwell_test_data_home=$app_home/workflows/Cromwell/test_data
if [ -d $cromwell_test_data_home ]; then
ln -s ${cromwell_test_data_home} ${io_home}/public/cromwell
fi

nextflow_test_data_home=$app_home/workflows/Nextflow/test_data
if [ -d $nextflow_test_data_home ]; then
ln -s ${nextflow_test_data_home} ${io_home}/public/nextflow
fi
fi

echo "Generate Cromwell wdl imports.zip"
wdl_dirs=(
"data"
)

for wdl_dir in "${wdl_dirs[@]}"
do
cd $app_home/workflows/Cromwell/WDL/${wdl_dir}
zip -r imports.zip *.wdl
if [ "$?" != "0" ]; then
echo "Cannot create $app_home/workflows/Cromwell/WDL/${wdl_dir}/imports.zip!" 1>&2
exit 1
fi
done

echo "Setup LANL EDGE webapp ..."
#build client
echo "build client..."
Expand Down
10 changes: 10 additions & 0 deletions webapp/client/src/edge/project/forms/TextInput.js
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Expand Up @@ -12,6 +12,7 @@ export const TextInput = (props) => {

const {
register,
reset,
formState: { errors },
trigger,
} = useForm({
Expand Down Expand Up @@ -54,6 +55,15 @@ export const TextInput = (props) => {
}
}, []) // eslint-disable-line react-hooks/exhaustive-deps

useEffect(() => {
if (props.defaultValue) {
reset({ textInput: props.defaultValue })
} else {
reset({ textInput: '' })
}
setDoValidation(doValidation + 1)
}, [props.reset]) // eslint-disable-line react-hooks/exhaustive-deps

useEffect(() => {
//validate form
trigger().then((result) => {
Expand Down
8 changes: 4 additions & 4 deletions webapp/server/utils/cromwell.js
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Expand Up @@ -24,7 +24,7 @@ const generateInputs = async (projHome, projectConf, workflowConf) => {
// projectConf: project conf.js
// workflowList in utils/workflow
const workflowSettings = workflowList[projectConf.workflow.name];
const template = String(fs.readFileSync(`${config.CROMWELL.TEMPLATE_DIR}/${projectConf.category}/${workflowSettings.inputs_tmpl}`));
const template = String(fs.readFileSync(`${config.CROMWELL.TEMPLATE_DIR}/${workflowSettings.inputs_tmpl}`));
const params = { ...workflowConf, ...projectConf.workflow.input, outdir: `${projHome}/${workflowSettings.outdir}` };

if (projectConf.workflow.name === 'sra2fastq') {
Expand All @@ -35,8 +35,8 @@ const generateInputs = async (projHome, projectConf, workflowConf) => {
const inputs = ejs.render(template, params);
await fs.promises.writeFile(`${projHome}/pipeline_inputs.json`, inputs);
// render options template and write to pipeline_options.json
if (fs.existsSync(`${config.CROMWELL.TEMPLATE_DIR}/${projectConf.category}/${workflowSettings.options_tmpl}`)) {
const optionsTemplate = String(fs.readFileSync(`${config.CROMWELL.TEMPLATE_DIR}/${projectConf.category}/${workflowSettings.options_tmpl}`));
if (fs.existsSync(`${config.CROMWELL.TEMPLATE_DIR}/${workflowSettings.options_tmpl}`)) {
const optionsTemplate = String(fs.readFileSync(`${config.CROMWELL.TEMPLATE_DIR}/${workflowSettings.options_tmpl}`));
const options = ejs.render(optionsTemplate, params);
await fs.promises.writeFile(`${projHome}/pipeline_options.json`, options);
}
Expand All @@ -52,7 +52,7 @@ const submitWorkflow = (proj, projectConf, inputsize) => {
formData.append('workflowInputs', fs.createReadStream(`${projHome}/pipeline_inputs.json`));
// logger.debug(`workflowInputs${projHome}/pipeline_inputs.json`);

const imports = `${config.CROMWELL.WDL_DIR}/${projectConf.category}/${workflowList[projectConf.workflow.name].wdl_imports}`;
const imports = `${config.CROMWELL.WDL_DIR}/${workflowList[projectConf.workflow.name].wdl_imports}`;
const optionsJson = `${projHome}/pipeline_options.json`;

if (fs.existsSync(optionsJson)) {
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4 changes: 2 additions & 2 deletions webapp/server/utils/workflow.js
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,8 @@ const nextflowConfigs = {
const workflowList = {
default_wdl_version: '1.0',
sra2fastq: {
wdl: 'sra2fastq.wdl',
wdl_imports: 'imports.zip',
wdl: 'data/sra2fastq.wdl',
wdl_imports: 'data/imports.zip',
inputs_tmpl: 'data/sra2fastq_inputs.tmpl',
cromwell_calls: ['sra.sra2fastq'],
outdir: 'output/sra2fastq',
Expand Down
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